We applied the PCA using the set of 12,898 structure inference SNPs in the original nested case-control study of prostate cancer (PLCOca-PLCOco) and found that the top 4 PCs are strongly significant with P-values less than 10−4 based on the Tracy Widom test, while the 5th is borderline significant (Table 1). To further justify the existence of axes with large genetic variation, we conducted a new PCA on PLCOca-PLCOcn using the alternative 7,017 structure inference SNPs described above (Table S3). In this case, the first two PCs were highly significant, namely a Tracy-Widom test P-value <10−7, but the additional lower ranked PCs (third and onwards) had P-value larger than 0.05. It is notable that there is a significant correlation for the first, as well as the second PC between the two PCAs (with Spearman rank correlation coefficient larger than 0.5 and P-value less than 10−15). Since the lower ranked (third and onwards) PCs estimated by the smaller set of SNPs were not significant, their correlations with the ones estimated by the larger set of SNPs were not evaluated.
